A novel type of protein‒protein interaction domain, referred to as the prion-like low-complexity (LC) domain, transiently forms a homotypic or heterotypic cross-β polymeric condensed phase to perform crucial neuronal functions1, 2. The prion-like LC domain was originally found to assemble membrane-less organs such as RNA granules, nucleoli, and nuclear bodies by liquid‒liquid phase separation (LLPS). Proteins with prion-like LC domains are involved in various biological processes, including DNA transcription and replication, chromatin remodeling, nuclear pore passage, signal transduction, synaptic transmission, and cytoskeleton regulation3,4,5,6. To date, tau, TDP-43 and alpha-synuclein have been identified as prion-like LC proteins, and disease-associated mutations in the genes encoding these proteins are mainly in the prion-like LC domains. However, loss of cross-β interactions of prion-like LC domains, particularly loss of heterotypic interactions of the prion-like domains of disease-causing proteins and their prion-like interaction partners, contributes to neurodegeneration remains to be further investigated.
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder that affects approximately 1 in 10,000 babies born worldwide each year7,8. SMN protein deficiency results in the gradual loss of motor neurons in the anterior horn of the spinal cord and subsequent system-wide atrophy of skeletal muscles9. Survival motor neuron 1 (SMN1), has been identified as the gene responsible for SMA10. Herein, we found that SMN1 contains a prion-like LC domain in exons 6-7 that drives LLPS of gems and that SMA is caused by loss of the prion-like domain of SMN1. Furthermore, we found that defects in the prion-like LC domain of SMN1 causes not only condensatorypathy but also collapse of cellular cross-β networks, i.e., aberrant prion-like assembly of RNPs, and protein aggregation of the SMN interaction partners TDP-43 and PFN1.
A nearly identical copy of SMN1, SMN2, is normally expressed in all patients with SMA. Although a small amount of full-length protein that is identical to SMN1 is produced, an exon-splicing silencer bearing a C-to-T transition in exon 7 of SMN2 in all individuals skips exon 711, 12. We found that exon 7 deletion leads to loss of SMN1 prion-like activity. Thus, it is clear that loss of a prion-like domain, such as in SMA, can cause aberrant assembly of RNPs, multiple proteinopathies and neurodegeneration. Significantly, baicalein restores the ability of the SMNΔ7 protein, which is encoded by SMN2, to adopt a prion-like conformation, effectively restoring the cellular functions of SMN1 and ameliorating SMA in human dermal fibroblasts (HDFs) and a mouse model. Therapeutic drugs, such as baicalein, can restore prion-like interactions and phase condensation and therefore may contribute to more effective treatment of neurodegenerative diseases.
Deficiency of the Prion-Like Domain of SMN1 Causes Aberrant RNP Assembly, PFN1 and TDP-43 Aggregation
Biotinylated isoxazole (b-isox), a recently identified chemical probe, specifically recognizes cross-β prion-like polymers and sequentially precipitates with proteins harboring prion-like, low-complexity (LC) or phase-separated domains, such as TDP-43, Fus and tau2. To determine whether SMN is a prion-like LC protein, we initially incubated 100 mM b-isox with mes23.5 and 293T cell lysates at 4°C to chemically precipitate whole prion-like proteins and then analyzed the efficiency of SMN binding by Western blotting to assess the prion-like and phase transition potentials of SMN (Fig. 1a and Extended Data Fig. 1). Western blot analysis revealed that SMN was precipitated by b-isox (Fig. 1a). Subcellular fractionation analysis revealed that the major cross-β conformation of SMN recognized by b-isox was localized in the cytosol (Fig. 1a). SET and PFN1 were used as fractionation controls (Fig. 1a).
To locate the prion-like domain of SMN, we examined the capability of full-length SMN (SMN-FL) and a panel of exon-deleted SMN constructs to form gems, i.e., their LLPS capability. A map of the SMN variants and the results are shown in Fig. 1b. Only fragments containing the region encoding exons 6-7 formed visible granules (Fig. 1b, arrowhead). The dynamics of mCherry-SMNexon6-7 granules in living cells were further analyzed by time-lapse microscopy, and the trajectory of mCherry-SMNexon6-7 granules is shown in Fig. 1c. Most of the mCherry-SMNexon6-7 granules traveled within a limited region (Fig. 1c), and two independent mCherry-SMNexon6-7 granules occasionally underwent fission and fusion (Fig. 1d, arrowheads). The average speed of mCherry-SMNexon6-7 granules was ~0.8 µm/s. As the prion-like domain of SMN is located in exons 6-7, we inferred that the SMNΔ7 protein, which is encoded by SMN2, is an inactive prion-like SMN protein.
In addition to engaging in homotypic interactions to assemble membrane-less organelles, such as the gem described above, prion-like LC domains also engage in heterotypic cross-β interactions. We thus conducted a detailed examination of SMN-associated prion-like proteins in SMA models. First, we assessed the global changes in prion-like LC protein expression in SMA. Spinal cord lysates were collected from type I SMA-like mice and control littermates, and prion-like LC proteins were precipitated by b-isox and identified through LC-MS/MS13. Differential b-isox-bound proteins were subsequently analyzed by the DAVID Functional Annotation Bioinformatics Analysis (https://david.ncifcrf.gov/tools.jsp) database, and the enriched Gene Ontology (GO) terms were identified. In SMA mice, according to GO enrichment analysis (FDR-adjusted P £ 4.95E-5, Fig. 1e), the expression of b-isox-precipitated proteins involved in RNA binding and RNP assembly was reduced, indicating a key role for SMN in the prion-like assembly of RNPs14. Consistent with the results of GO enrichment analysis, 15 out of 48 downregulated proteins were RNA-binding proteins (Fig. 1e).
Next, immunofluorescence staining revealed that an SMN prion-like interaction partner, PFN1, formed cytosolic aggregates in SMA patient-derived human dermal fibroblasts (HDFs) (Fig. 1f). PFN1 is a known ALS-causing protein; it becomes misfolded and forms cytosolic misfolded aggregates in patients with ALS15,16,17. To confirm that deficiency of one prion-like protein abolishes the prion-like folding of its interaction partners, causing them to form aggregates, we examined the localization of another prion-like interaction partner of SMN1, TDP-43, in spinal cord motor neurons in SMA mice (Fig. 1g). TDP-43 is a key molecule in ALS, as misfolded TDP-43 aggregates have been observed in ~80% of ALS patients18. Indeed, the results of TDP-43 immunofluorescence showed TDP-43 mislocalization in the cytosol (arrowhead) and deposition on the nuclear envelope (arrow) in the motor neurons of SMA mice. Of note, the aggregation of ALS-causing proteins in SMA has never been reported. These findings related to PFN1 and TDP-43 reveal that SMA and ALS share a common etiology.
Finally, we treated healthy HDFs with b-isox to interfere with the cross-β interactions of prion-like LC proteins and found that the number of gems was significantly reduced. Conversely, the number of PFN1 aggregates increased in a dose-dependent manner, confirming that disrupting prion-like cross-β interactions can lead to protein aggregates (Fig. 1h).
Baicalein-Mediated Conformational Alteration of SMN2 Triggers Phase Separation and Endows SMN2 with SMN1 Prion-Like Functions
In searching for an activator to restore SMN cross-β interactions, we found that baicalein normalizes the assembly of gems in type III SMA patient-derived HDFs by screening a chemical library (Fig. 2a)19. On the other hand, we noticed that after treating SMA patient-derived HDFs with baicalein, TDP-43 aggregates disappeared (Fig. 2b). Statistical analysis of data related to the effect of baicalein on the formation of gems is shown in Fig. 2c. As SMA patient-derived HDFs express only the SMN2 protein, we speculated that baicalein restores the formation of gems in SMA patient-derived HDFs by altering the conformation of the nonfunctional prion-like C-terminus of SMN2. We used the b-isox precipitation assay to assess the cross-β conformation of SMN2 in vivo and found that the cross-β conformation of SMN2 in baicalein-treated SMA patient-derived HDFs was the same as that of SMN-FL (Fig. 2d). These results suggest that baicalein may endow the nonfunctional SMN2 C-terminus with the ability to adopt a prion-like conformation.
We next assessed whether these SMN2 proteins with baicalein-induced restoration of prion-like activity can perform the unique cellular functions of SMN1. We measured the length of axons of neurons transfected with SMNΔ7 in the presence or absence of baicalein, as neurons transfected with SMNΔ7 extend significantly shorter neurites than those transfected with SMN-FL20, 21. Indeed, baicalein increased the length of axons from NSC34 cells expressing SMNΔ7 by approximately 2 fold (Fig. 2e); the results of statistical analysis are shown in Fig. 2f. As the protein half-life of SMNΔ7 is two-fold shorter than that of SMN-FL in cells, we examined the stability of the SMNΔ7 protein in the presence of baicalein and found that baicalein significantly increased the stability of the SMNΔ7 protein (Fig. 2g, arrow) 22. Additionally, as PFN1 is known to effectively interact with SMN but not SMNΔ7, we analyzed the interactions of SMNΔ7 and PFN1 in baicalein-treated cells by coimmunoprecipitation (Fig. 2h) 15,16. The results showed that in the presence of baicalein, the interaction between PFN1 and SMNΔ7 was significantly increased (Fig. 2h, arrowhead).
To comprehensively identify the pharmacological targets of baicalein in SMA, we collected protein lysates from NSC34 cells treated with or without baicalein and then precipitated the proteins with b-isox. The proteins precipitated by b-isox were then identified by LC‒MS/MS. Differential protein expression was subsequently analyzed by the DAVID database, and enriched GO terms were identified. Importantly, in baicalein-treated NSC34 cells, the top 5 upregulated GO terms were mostly related to the cellular functions of Smn, including Sm core formation, SnRNP assembly, RNA binding, and RNA splicing (FDR adjusted P £ 1.09E-9, Fig. 2i). Among the 71 proteins whose expression was regulated by baicalein, 26 were directly associated with Smn or involved in Smn complexes (Fig. 2i)23. Together with the results in Figure 2, these findings suggest that baicalein endows SMN2 with prion-like bioactivity, allowing it to behave similarly to SMN1.
Baicalein Improves Survival and Rescues Gem Assembly and Motor Neuron Function in SMA Mice
To determine whether the in vitro findings could be recapitulated in vivo, we administered baicalein (13.6 mg/kg/d) or DMSO (control) to late-onset type III SMA model mice daily by intraperitoneal injection19. After 4 weeks of treatment, histological analysis of lumbar spinal sections from SMA mice confirmed an increase in the ChAT-positive motor neuron number (Fig. 3a, P=0.0435) and recovery of nuclear gem formation (Fig. 3a, bottom, P=0.0063, labeled by arrowheads in Fig. 3a).
We found that SMN protein levels but not SMN mRNA levels were increased in various tissues from baicalein-treated SMA mice compared with those from control SMA mice (Fig. 3b) (Extended Data Fig. 2), confirming that baicalein increases the protein stability of SMND7, consistent with the data shown in Fig. 2g. Beginning at 7 months of age, we treated type III SMA mice with baicalein for four months, which improved mouse survival (P=0.048) (Fig. 3c). A reduction in the evoked compound muscle action potential (CMAP) amplitude upon sciatic nerve stimulation was observed in control SMA mice (Fig. 3d, left, P=0.0201), but this phenomenon was abolished in baicalein-treated SMA mice (Fig. 3d, right, P=0.3326). Baicalein-treated SMA mice showed better motor performance than control mice in both the fixed-speed and accelerating rotarod tests, as determined by measuring the latency to fall (Fig. 3e and f). Fluorogold retrograde tracing of spinal motor neurons revealed a higher motor neuron density within the anterior horn (Fig. 3g, left, P=0.0114) and more large a-motor neurons (Fig. 3g, right, P=0.0037) in baicalein-treated mice than in control SMA mice. Significantly, baicalein treatment increased the axonal innervation of neuromuscular junctions (NMJs) in the hamstring muscles of SMA mice (Fig. 3h, P=0.04).
Next, we administered baicalein (13.6 mg/kg/d) or DMSO (control) to early-onset type I SMA model mice daily by intraperitoneal injection beginning at birth. We expected that the therapeutic efficacy of baicalein on type I SMA mice was weaker, as SMN2 protein levels are lower in type I SMA than in type III SMA. After baicalein treatment, the motor function of SMA mice, including the righting time, tube score, and tilting score, was improved on the 6th postnatal day (P<0.05), and the results were similar to those for heterozygous littermates treated with or without baicalein (Extended Data Fig. 3). On the 8th postnatal day, the motor function of baicalein-treated SMA mice was better than that of untreated SMA mice in the tube test (P=0.009) but not in the turnover test (P=0.065) or negative geotaxis test (P=0.58) (Extended Data Fig. 2). However, baicalein-treated type I SMA mice showed lifespans (8.8±0.4 vs. 7.9±0.2 days; P=0.13) and body weight gains that were similar to those of control SMA mice. The weaker effects of baicalein treatment on type I SMA mice than on type I SMA mice supports that baicalein targets to SMN2, endowing it with prion-like activity to perform the prion-like functions of SMN1 in vivo.